From c9039705775edcd7ce65485295b9193607cb0789 Mon Sep 17 00:00:00 2001
From: fellen31 <felixlenner@gmail.com>
Date: Tue, 5 Nov 2024 16:46:59 +0100
Subject: [PATCH] update methylation config

---
 subworkflows/local/methylation/tests/nextflow.config | 2 +-
 tests/.nftignore                                     | 4 ++++
 tests/samplesheet.nf.test.snap                       | 6 +-----
 tests/samplesheet_multisample_bam.nf.test.snap       | 6 +-----
 tests/samplesheet_multisample_ont_bam.nf.test.snap   | 6 +-----
 5 files changed, 8 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/methylation/tests/nextflow.config b/subworkflows/local/methylation/tests/nextflow.config
index 45b920fe..b977ef2a 100644
--- a/subworkflows/local/methylation/tests/nextflow.config
+++ b/subworkflows/local/methylation/tests/nextflow.config
@@ -5,7 +5,7 @@ params {
 
 process {
 
-    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT' {
+    withName: 'SHORT_VARIANT_CALLING:DEEPVARIANT_RUNDEEPVARIANT' {
         ext.args = { [
             '--model_type PACBIO',
             "--sample_name=${meta.id}",
diff --git a/tests/.nftignore b/tests/.nftignore
index 82f09b18..827e5c29 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -6,6 +6,10 @@ multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_data/multiqc_somalier.txt
 multiqc/multiqc_data/somalier_*_plot.txt
 multiqc/multiqc_data/multiqc_sources.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt
+multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt
 multiqc/multiqc_plots/**/*.{pdf,svg,txt,png}
 multiqc/multiqc_report.html
 paraphase/**/*.{vcf.gz,tbi,bam,bai,json}
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
index 73edb4ca..a19a7627 100644
--- a/tests/samplesheet.nf.test.snap
+++ b/tests/samplesheet.nf.test.snap
@@ -525,10 +525,6 @@
                 "HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi:md5,e1418c8075da8831a52e0cd56ceb910e",
                 "bcftools-stats-subtypes.txt:md5,2c23b13117d584b4f424c2bc56dfa4ba",
                 "bcftools_stats_indel-lengths.txt:md5,bea599c38615af6a033ea3a4436d52c5",
-                "bcftools_stats_vqc_Count_Indels.txt:md5,301a8bd32f3fb6f00b17de6546e01d58",
-                "bcftools_stats_vqc_Count_SNP.txt:md5,6b9448fe119d4369f543be58525c093d",
-                "bcftools_stats_vqc_Count_Transitions.txt:md5,8ebc25ff2770562063f93ebb60300a94",
-                "bcftools_stats_vqc_Count_Transversions.txt:md5,0fe48d84efedd2090b3e9774e2fa805b",
                 "fastqc-status-check-heatmap.txt:md5,f98c3e5395cfd3061b3228a97ba86043",
                 "fastqc_adapter_content_plot.txt:md5,85e76640241ce1fd8e3bbf42eb3fa447",
                 "fastqc_per_base_n_content_plot.txt:md5,c9e46e2888289c319e1b9f412cb0d8e5",
@@ -666,6 +662,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-05T16:30:14.121766168"
+        "timestamp": "2024-11-05T16:51:01.978272264"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
index f7c6027b..cbadd83b 100644
--- a/tests/samplesheet_multisample_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -644,10 +644,6 @@
                 "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,f569a923cc5204df5dc495354ab83a13",
                 "bcftools-stats-subtypes.txt:md5,5b9c985c35950dfb8cd7827fc8d524c4",
                 "bcftools_stats_indel-lengths.txt:md5,9272a5340f808c3f5874f1b2fd18da6c",
-                "bcftools_stats_vqc_Count_Indels.txt:md5,e80a75948a709d9c0740952af0eac322",
-                "bcftools_stats_vqc_Count_SNP.txt:md5,9d197874867d3635db9accd9c48811d3",
-                "bcftools_stats_vqc_Count_Transitions.txt:md5,3118dafd58775ce162a4a6193bd711a6",
-                "bcftools_stats_vqc_Count_Transversions.txt:md5,51e3083293ec9a9058cf59eb804d04bb",
                 "fastqc-status-check-heatmap.txt:md5,20c6520b895e05df6cfeab492819e94a",
                 "fastqc_adapter_content_plot.txt:md5,8f9e7b3e1e31caeb58b0fbf31624ea53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,9b021bffa0a2d100fdbe637fa7c40a62",
@@ -876,6 +872,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-05T16:32:09.134642798"
+        "timestamp": "2024-11-05T16:52:58.066116844"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
index 6bdaee0a..badb89df 100644
--- a/tests/samplesheet_multisample_ont_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -489,10 +489,6 @@
                 "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,3d97d016882c99e4e21112fc76ceb2a2",
                 "bcftools-stats-subtypes.txt:md5,1a8c8da19e5bc947cfb77de3683c8c00",
                 "bcftools_stats_indel-lengths.txt:md5,cc976b96114f0b68daffec58a7643d53",
-                "bcftools_stats_vqc_Count_Indels.txt:md5,8b79c69658c50946467ec8f24c80ccea",
-                "bcftools_stats_vqc_Count_SNP.txt:md5,328484ca8612a624a082ca261b76df0f",
-                "bcftools_stats_vqc_Count_Transitions.txt:md5,028c047ee7b455ffa97235f5e2544547",
-                "bcftools_stats_vqc_Count_Transversions.txt:md5,816aba2bc2b521534d8ff2105364faae",
                 "fastqc-status-check-heatmap.txt:md5,03e5dc3abd2f2599a7bb03739dd5ca86",
                 "fastqc_adapter_content_plot.txt:md5,00c7bec7dd9304848f7d891d7d1fab7f",
                 "fastqc_overrepresented_sequences_plot.txt:md5,6f0148406e9d5358bf37375b33a4bc01",
@@ -620,6 +616,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-11-05T16:33:58.630674994"
+        "timestamp": "2024-11-05T16:54:45.933051024"
     }
 }
\ No newline at end of file